I have done an extensive update of the lecture slides on codon models for 2016 & 2017. The update includes greater coverage of the mechanistic process of codon evolution (via the MutSel framework). Because there is now less detail about fitting codon models to real data, I have included links to the 2015 slides below; these slides provide more practical information about the powers and pitfalls of inference under codon models.

The lab exercises (PAML demo) have been published to a small website (link below). The site contains some additional resources. Please note that presentations may change up until the moment the lecture or lab begins. I will post modified PDFs after each talk.

If you have some experience with codon models, and want to try out a tutorial for more advanced materials then use the link below to download an archive for a complete different set of PAML activities. This tutorial focuses on detecting episodic protein evolution via Branch-Site Model A. The tutorial also includes activities about (i) detecting MLE instabilities, (ii) carrying out robustness analyses, and (iii) use of smoothed bootstrap aggregation (SBA). The protocols for each activity are presented in Protocols in Bioinformatics UNIT 6.15. The included PDF file for UNIT 6.16 also presents recommendations for "best practices" when carrying out a large-scale evolutionary survey for episodic adaptive evolution by using PAML. The files required for this "alternative lab" are available via Bitbucket repository. The repository link is given below.

Large-scale evolutionary surveys are now commonplace. But with the use of progressively more complex codon models, these surveys are fraught with perils. Complex models are more prone to statistical problems such as MLE irregularities, and some can be quite sensitive to model misspecification. UNIT 6.16 (see above) provides some recommended "best practices" for a 2-phase approach to quality control and robustness in evolutionary surveys. We have applied these to a large scale survey for functional divergence in nuclear receptors during homing evolution, and we used experimental approaches to investigate hypotheses about the role of a particular nuclear receptor (NR2C1) as a key modulator of developmental pluripotnetiality during hominid evolution. The paper that illustrates the power of such an evolutionary surgery, and the importance of an experimental design having explicit protocols for "best practices", is given below.